Back to Multiple platform build/check report for BioC 3.12
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for basecallQC on tokay1

This page was generated on 2020-10-24 11:01:07 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE basecallQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 116/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.13.0
Thomas Carroll
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: master
Last Commit: 63dc0f4
Last Changed Date: 2020-04-27 15:06:59 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: basecallQC
Version: 1.13.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:basecallQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings basecallQC_1.13.0.tar.gz
StartedAt: 2020-10-24 00:54:15 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 01:03:22 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 547.0 seconds
RetCode: 0
Status:  OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:basecallQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings basecallQC_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/basecallQC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'basecallQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'basecallQC' version '1.13.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'basecallQC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
reportBCL             9.38   0.55   19.95
demuxBarplot          7.64   0.14    7.78
basecallQC            6.91   0.10    7.00
demuxBoxplot          6.05   0.01    6.07
baseCallMetrics       5.51   0.51    6.13
passFilterTileplot    5.97   0.03    6.00
makeFQTable           5.87   0.11    5.99
passFilterBar         5.80   0.11    5.90
summaryConvStatsTable 5.75   0.02    5.77
passFilterBoxplot     5.61   0.13    5.74
summaryDemuxTable     5.31   0.01    5.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
reportBCL             12.84   0.48   13.77
baseCallMetrics        8.15   0.08    8.24
passFilterTileplot     7.34   0.02    7.36
summaryDemuxTable      7.23   0.02    7.25
summaryConvStatsTable  6.90   0.00    6.89
basecallQC             6.51   0.00    6.57
demuxBoxplot           6.48   0.00    6.48
makeFQTable            6.39   0.01    6.41
demuxBarplot           6.27   0.00    6.27
passFilterBoxplot      5.87   0.01    5.89
passFilterBar          5.54   0.02    5.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

basecallQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/basecallQC_1.13.0.tar.gz && rm -rf basecallQC.buildbin-libdir && mkdir basecallQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=basecallQC.buildbin-libdir basecallQC_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL basecallQC_1.13.0.zip && rm basecallQC_1.13.0.tar.gz basecallQC_1.13.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  659k  100  659k    0     0  8101k      0 --:--:-- --:--:-- --:--:-- 8454k

install for i386

* installing *source* package 'basecallQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'basecallQC'
    finding HTML links ... done
    BCL2FastQparams                         html  
    baseCallMetrics                         html  
    basecallQC                              html  
    createBCLcommand                        html  
    createBasemasks                         html  
    demultiplexMetrics                      html  
    demuxBarplot                            html  
    demuxBoxplot                            html  
    indexlengths                            html  
    interOpsReport                          html  
    makeFQTable                             html  
    passFilterBar                           html  
    passFilterBoxplot                       html  
    passFilterTileplot                      html  
    readlengths                             html  
    reportBCL                               html  
    summaryConvStatsTable                   html  
    summaryDemuxTable                       html  
    validateBCLSheet                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'basecallQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'basecallQC' as basecallQC_1.13.0.zip
* DONE (basecallQC)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'basecallQC' successfully unpacked and MD5 sums checked

Tests output

basecallQC.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
> 
> test_check("basecallQC")
== testthat results  ===========================================================
[ OK: 5 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  21.98    1.87   23.96 

basecallQC.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
> 
> test_check("basecallQC")
== testthat results  ===========================================================
[ OK: 5 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  22.28    0.64   22.90 

Example timings

basecallQC.Rcheck/examples_i386/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.270.180.44
baseCallMetrics5.510.516.13
basecallQC6.910.107.00
createBCLcommand0.620.000.62
createBasemasks0.640.000.64
demultiplexMetrics0.110.000.11
demuxBarplot7.640.147.78
demuxBoxplot6.050.016.07
indexlengths0.030.000.03
interOpsReport0.020.000.01
makeFQTable5.870.115.99
passFilterBar5.800.115.90
passFilterBoxplot5.610.135.74
passFilterTileplot5.970.036.00
readlengths0.030.010.05
reportBCL 9.38 0.5519.95
summaryConvStatsTable5.750.025.77
summaryDemuxTable5.310.015.33
validateBCLSheet0.110.000.11

basecallQC.Rcheck/examples_x64/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.390.000.39
baseCallMetrics8.150.088.24
basecallQC6.510.006.57
createBCLcommand0.490.000.48
createBasemasks0.470.000.47
demultiplexMetrics0.070.000.06
demuxBarplot6.270.006.27
demuxBoxplot6.480.006.48
indexlengths0.030.000.03
interOpsReport0.020.000.02
makeFQTable6.390.016.41
passFilterBar5.540.025.55
passFilterBoxplot5.870.015.89
passFilterTileplot7.340.027.36
readlengths0.050.000.04
reportBCL12.84 0.4813.77
summaryConvStatsTable6.900.006.89
summaryDemuxTable7.230.027.25
validateBCLSheet0.120.000.12